Synthetic CpG oligonucleotides are promising components of immunomodulatory drugs for the treatment and prophylaxis of infectious diseases, cancers, and allergies. Phosphorothioate modification stabilizes these compounds, contributing to the achievement of a clinical effect, but at the same time changes their immunomodulatory properties. We used the diffusible fluorescent dye dihydroethidium and the non-diffusible 6-carboxy-2′,7′dihydrochlorofluorescein diacetate and cytochrome c probes to demonstrate that it is the phosphorothioate backbones that determine the pronounced nonspecific pro-oxidant effect of CpG ODN on neutrophils. At the same time, as was shown using diaminofluorescein diacetate, the potentiation of nitric oxide synthesis in these leucocytes by CpG ODN class A strictly depends on the presence of CpG motifs and a palindromic “hairpin”. The results obtained will contribute to a more complete understanding of the physiological action of therapeutic agents based on synthetic CpG oligonucleotides.